2.2 DNA extraction
The content of each capsule was transferred to a 50 mL Falcon tube that
was centrifugated for 15 min at 15,000 g. The supernatant was removed,
leaving 15 mL of liquid. Then, alcohol precipitation was performed by
adding 33 mL of ethanol and 1.5 mL of 3M sodium acetate were added to
each 50 mL tube, and samples were stored for 24h at -20°C. After
centrifugation for 15 min at 15,000 g, the supernatant was discarded.
360 µL of ATL Buffer of the DNeasy Blood & Tissue Extraction Kit
(Qiagen) were added to the pellet, thoroughly mixed, and transferred in
a 2 mL tube. The remaining steps of the DNA extraction were carried out
using the NucleoSpin soil kit (Macherey Nagel) from step 6. The DNA was
eluted with 100 µL of SE buffer twice. Two types of extraction negative
controls were performed during each extraction session, the first one
starting with a 50 mL Falcon tube filled by CL1 buffer, and the second
one starting with 360 µL of ATL Buffer of the DNeasy Blood & Tissue
Extraction Kit (Qiagen) in a 2 mL tube.